I know you stated that you reviewed the NCDrill file, and the holes are not present, but can you verify it one more time by generating a plot file from the NCDrill file then loading it into the design as an overlay.
From a DOS Prompt type the following: explot your_ncdrill_file.drl
This will generate an Intermediate Plot file (IPF) for the NCDrill file. You can then load the .PLT file generated into your design using File > Import > IPF... and it can used as an overlay to verify which holes are missing. The default location of the loaded plot data is under Class Manufacturing / Subclass Pen# or you could re-target its load location but changing the Class and Subclass under the Options tab after selecting the .plt file and just before indicating a load point of the plot.
Can you post the Padstack Summary report (Reports > Padstack Summary) for the padstack that is not generating points in the NCdrill file. (Tools > Padstack > Modify Design Padstacks) padstack
Hope this helps,